`ld` error when installing hdp package in R

Question

I am try to install the hdp package by Nicola Robers using the following command in R:

devtools::install_github("nicolaroberts/hdp", build_vignettes = TRUE)

This used to get compiled and installed fine when I had the R version 3.6.2 and gcc version 9.2.1 on an (Arch) Linux machine. After updating the system to R 4.0.0 and gcc 10.1.0, the installation fails with the following message:

* installing *source* package ‘hdp’ ...
** using staged installation
** libs
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R-base.c -o R-base.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R-conparam.c -o R-conparam.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R-dp.c -o R-dp.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R-hdp.c -o R-hdp.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R-hdpMultinomial_iterate.c -o R-hdpMultinomial_iterate.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R-multinomial.c -o R-multinomial.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R-utils.c -o R-utils.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c randutils.c -o randutils.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o hdp.so R-base.o R-conparam.o R-dp.o R-hdp.o R-hdpMultinomial_iterate.o R-multinomial.o R-utils.o randutils.o -L/usr/lib64/R/lib -lR
/usr/bin/ld: R-conparam.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here
/usr/bin/ld: R-dp.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here
/usr/bin/ld: R-hdp.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here
/usr/bin/ld: R-hdpMultinomial_iterate.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here
/usr/bin/ld: R-multinomial.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here
/usr/bin/ld: R-utils.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here
/usr/bin/ld: randutils.o:(.bss+0x0): multiple definition of `DEBUG'; R-base.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R//make/shlib.mk:6: hdp.so] Error 1
ERROR: compilation failed for package ‘hdp’

The individual files are compiling fine, but the linking seems to fail. Any idea on how to go about debugging what is missing?

passerby51 passerby51 · Accepted Answer · 2020-05-30T20:22:11

In case someone else runs into this issue: I manged to compile it by commenting all the references to the debug printing code. I commented all lines with rdebug* and DEBUG. These functions are mainly defined in R-utils.h. It still would be nice to find a better solution. There seems to be a circular definition of the DEBUG?

`ld` error when installing hdp package in R

1 Answers